They gave you basically auction price for your trade, so they don't need to see it beforehand. Then asking you to document the condition is just for their records, highly doubt they took anything into consideration. May not have even read it.
As far as accessories, as others have said, take what you want or can sell, leave or throw-away the rest. Unless it's nearly impossible to remove the EMS, I'd definitely consider doing that and install it on the new unit (assuming both are same amperage). That is one thing I'd consider worth the hassle and their offer sure didn't take it into consideration.
Mike